Strain identifier

BacDive ID: 14293

Type strain: Yes

Species: Sphingosinicella microcystinivorans

Strain Designation: Y2

Strain history: CIP <- 2006, JCM <- 2005, T. Maruyama, Marine Works Japan Ltd., Yokohama, Japan: strain Y2

NCBI tax ID(s): 335406 (species)

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General

@ref: 8320

BacDive-ID: 14293

DSM-Number: 19791

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped

description: Sphingosinicella microcystinivorans Y2 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from eutrophic lake.

NCBI tax id

  • NCBI tax id: 335406
  • Matching level: species

strain history

@refhistory
8320<- P. Kämpfer, Univ. Giessen <- T. Maruyama
67770T. Maruyama Y2.
67771<- HD PARK
120947CIP <- 2006, JCM <- 2005, T. Maruyama, Marine Works Japan Ltd., Yokohama, Japan: strain Y2

doi: 10.13145/bacdive14293.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Sphingomonadales
  • family: Sphingosinicellaceae
  • genus: Sphingosinicella
  • species: Sphingosinicella microcystinivorans
  • full scientific name: Sphingosinicella microcystinivorans Maruyama et al. 2006

@ref: 8320

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Sphingosinicellaceae

genus: Sphingosinicella

species: Sphingosinicella microcystinivorans

full scientific name: Sphingosinicella microcystinivorans Maruyama et al. 2006 emend. Geueke et al. 2007

strain designation: Y2

type strain: yes

Morphology

cell morphology

@refgram staincell widthcell shapemotilityconfidence
31549negative0.3-0.7 µmrod-shapedyes
67771negative
69480negative99.992
120947negativeoval-shapedno

colony morphology

  • @ref: 120947

pigmentation

  • @ref: 31549
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8320R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
37472MEDIUM 328- for nutrient agaryesDistilled water make up to (1000.000 ml);Agar (15.000 g);Peptone (5.000g);Beef extract (3.000 g)
120947CIP Medium 328yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=328

culture temp

@refgrowthtypetemperaturerange
8320positivegrowth28mesophilic
31549positivegrowth10-37
31549positiveoptimum30mesophilic
37472positivegrowth30mesophilic
67770positivegrowth30mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
31549positivegrowth07-09alkaliphile
31549positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31549aerobe
67771aerobe
120947obligate aerobe

spore formation

@refspore formationconfidence
31549no
69481no100
69480no99.995

observation

@refobservation
31549aggregates in chains
67771quinones: Q-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12094717632nitrate-reduction
12094716301nitrite-reduction

metabolite production

  • @ref: 120947
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
31549catalase+1.11.1.6
31549cytochrome oxidase+1.9.3.1
120947oxidase+
120947alcohol dehydrogenase-1.1.1.1
120947catalase+1.11.1.6
120947lysine decarboxylase-4.1.1.18
120947ornithine decarboxylase-4.1.1.17
120947urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase+3.4.11.3
68382trypsin+3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
120947-+++-++++-++-----+--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinenthost species
8320eutrophic lakeLake SuwaJapanJPNAsia
67770Toxic Microcystis blooming lakeLake SuwaJapanJPNAsiaMicrocystis
67771From a toxic Microcystis blooming lakeLake SuwaJapanJPNAsia
120947Environment, Blooming lakeSuwa lakeJapanJPNAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Lake (large)

taxonmaps

  • @ref: 69479
  • File name: preview.99_29701.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_14601;97_17816;98_22148;99_29701&stattab=map
  • Last taxonomy: Sphingosinicella
  • 16S sequence: AB084247
  • Sequence Identity:
  • Total samples: 17610
  • soil counts: 5974
  • aquatic counts: 7685
  • animal counts: 2606
  • plant counts: 1345

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
83201Risk group (German classification)
1209471Risk group (French classification)

Sequence information

16S sequences

  • @ref: 8320
  • description: Sphingosinicella microcystinivorans gene for 16S rRNA, partial sequence, strain:Y2
  • accession: AB084247
  • length: 1449
  • database: ena
  • NCBI tax ID: 335406

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sphingosinicella microcystinivorans strain DSM 19791335406.3wgspatric335406
66792Sphingosinicella microcystinivorans DSM 197912770939615draftimg335406
67770Sphingosinicella microcystinivorans DSM 19791GCA_003634215scaffoldncbi335406

GC content

@refGC-contentmethod
3154963.6
6777063.6-63.7high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno97.359no
anaerobicno98.484yes
halophileno89.048no
spore-formingno95.131yes
glucose-utilyes73.308no
motileyes86.908yes
flagellatedno85.506no
thermophileno96.502no
aerobicyes87.358no
glucose-fermentno93.511no

External links

@ref: 8320

culture collection no.: DSM 19791, JCM 13185, KCTC 12019, CIP 109169, NCIMB 14270

straininfo link

  • @ref: 83446
  • straininfo: 289871

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16403871Sphingosinicella microcystinivorans gen. nov., sp. nov., a microcystin-degrading bacterium.Maruyama T, Park HD, Ozawa K, Tanaka Y, Sumino T, Hamana K, Hiraishi A, Kato KInt J Syst Evol Microbiol10.1099/ijs.0.63789-02006Bacterial Toxins/metabolism, Base Composition, Fatty Acids, *Fresh Water, Glycosphingolipids, Japan, Microcystins, Molecular Sequence Data, Peptides, Cyclic/*metabolism, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Homology, Nucleic Acid, Species Specificity, Sphingomonadaceae/chemistry/*classification/isolation & purification/physiology, UbiquinoneMetabolism
Phylogeny26315363Sphingosinicella cucumeris sp. nov., isolated from soil of a cucumber garden.Akter S, Du J, Won K, Yin CS, Kook M, Yi THAntonie Van Leeuwenhoek10.1007/s10482-015-0572-62015Base Composition, *Cucumis sativus/microbiology, DNA, Bacterial, Fatty Acids/chemistry, Lipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Sphingomonadaceae/chemistry/*classification/isolation & purification/physiologyTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
8320Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19791)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19791
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
31549Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2784028776041
37472Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6880
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68382Automatically annotated from API zym
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.https://microbeatlas.org/MicrobeAtlas 1.0 beta
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
83446Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID289871.1StrainInfo: A central database for resolving microbial strain identifiers
120947Curators of the CIPCollection of Institut Pasteur (CIP 109169)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109169